uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools
Class TotalExonLengthAnalysisTools

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools

public class TotalExonLengthAnalysisTools
extends java.lang.Object

class which contains computing tools for TotalExonLengthAnalysis.

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
TotalExonLengthAnalysisTools()
           
 
Method Summary
private static java.util.HashMap getGmHashOfEqualGms(java.util.ArrayList _arrListOfGmRegions)
          method which calculates hash of gene models pointing to number of equal gms (including the genemodel itself)
private static java.util.HashMap getGmHashOfLocations(java.util.ArrayList _arrListOfGmRegions)
          method which calculates hash of locations pointing to their array of gms with the same location (equal genemodels).
static java.util.HashMap getTlExLengthScoredGmHash(int debug, java.util.ArrayList _arrListOfGMRegions)
          method which returns total exon length of a genemodel.
private static double getTotalExonLengthScore(GeneModel gm, java.util.HashMap gmHashOfEqualGms)
          method which calculates score for a genemodel using the total exon length as scoring system.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

TotalExonLengthAnalysisTools

public TotalExonLengthAnalysisTools()
Method Detail

getTlExLengthScoredGmHash

public static java.util.HashMap getTlExLengthScoredGmHash(int debug,
                                                          java.util.ArrayList _arrListOfGMRegions)
method which returns total exon length of a genemodel. Total exon length means accumulated length of all exons within a genemodel excluding introns.

Parameters:
debug - debugging mode
_arrListOfGMRegions - ArrayList of genemodel regions
Returns:
hash of genemodels pointing to their total exon length

getTotalExonLengthScore

private static double getTotalExonLengthScore(GeneModel gm,
                                              java.util.HashMap gmHashOfEqualGms)
method which calculates score for a genemodel using the total exon length as scoring system. Genemodel which have equal companions get a higher score. This score is calculated by using the length of the sequence and multiplying it by the number of equal genemodels. The reason for this implementation is that in the case of overlapping genemodels rather equal genemodels should be chosen.

Parameters:
gm - genemodel
gmHashOfEqualGms - HashMap of genemodels pointing to the number of equal genemodels (including the genemodel itself)
Returns:
genemodel score using the total exon length scoring system

getGmHashOfEqualGms

private static java.util.HashMap getGmHashOfEqualGms(java.util.ArrayList _arrListOfGmRegions)
method which calculates hash of gene models pointing to number of equal gms (including the genemodel itself)

Parameters:
_arrListOfGmRegions - ArrayList of genemodel regions
Returns:
HashMap of genemodel pointing to the number of equal genemodels

getGmHashOfLocations

private static java.util.HashMap getGmHashOfLocations(java.util.ArrayList _arrListOfGmRegions)
method which calculates hash of locations pointing to their array of gms with the same location (equal genemodels).

Parameters:
_arrListOfGmRegions - ArrayList of genemodel regions
Returns:
HashMap of Locations pointing to ArrayList of genemodels with this particular Location